The ability to predict the structural modifications of materials resulting from a broad range of irradiation scenarios would have a positive impact on many fields of science and technology. Established techniques for modelling large atomic systems, such as classical molecular dynamics, are limited by the neglect of the electronic degrees of freedom which restricts their application to irradiation events that primarily interact with atomic nuclei. Ab initio methods, on the other hand, include electronic degrees of freedom, but the requisite computational costs restrict their application to relatively small systems. Recent methodological developments aimed at overcoming some of these limitations are based on methods that couple atomistic models to a continuum model for the electronic energy, where energy is exchanged between the nuclei and electrons via electronic stopping and electron-phonon coupling mechanisms. Such two-temperature molecular dynamics models, as they are known, make it practicable to simulate the effects of electronic excitations on systems with millions, or even hundreds of millions, of atoms. They have been used to study laser irradiation of metallic films, swift heavy ion irradiation of metals and semiconductors, and moderately high ion irradiation of metals. In this review we describe the two-temperature molecular dynamics methodology and the various practical considerations required for its implementation. We provide example applications of the model to multiple irradiation scenarios that accommodate electronic excitations. We also describe the challenges of including the effects of the modification of the interatomic interactions, due to the excitation of electrons, in the simulations and how these challenges can be overcome.